Threshold Filtering

Threshold filters, following the guidance of Florida Department of Environmental Protection’s (FDEP) Division of Environmental Assessment and Restoration (DEAR) are used to exclude specific results values from the SEACAR Analysis. Based on the threshold filters, Quality Assurance / Quality Control (QAQC) Flags are inserted into the SEACAR_QAQCFlagCode and SEACAR_QAQC_Description columns of the export data. The Include column indicates whether the QAQC Flag will also indicate that data are excluded from analysis. No data are excluded from the data export, but the analysis scripts can use the Include column to exclude data (1 to include, 0 to exclude).

Continuous Water Quality threshold values
Parameter Name	Units	Low Threshold	High Threshold	Sensor Type
Dissolved Oxygen	mg/L	0	50	YSI EXOs
Dissolved Oxygen	mg/L	0	50	Analysis Only - 2022-04-04
Dissolved Oxygen	mg/L	0	50	6600 Series
Salinity	ppt	0	70	6600 Series
Salinity	ppt	0	70	YSI EXOs
Salinity	ppt	0	70	Analysis Only - 2022-04-04
Water Temperature	Degrees C	-5	45	YSI EXOs
Water Temperature	Degrees C	-5	45	Analysis Only - 2022-04-04
Water Temperature	Degrees C	-5	45	6600 Series
pH	pH	2	14	Analysis Only - 2022-04-04
pH	pH	2	14	6600 Series
pH	pH	2	14	YSI EXOs
Dissolved Oxygen Saturation	%	0	500	YSI EXOs
Dissolved Oxygen Saturation	%	0	500	6600 Series
Dissolved Oxygen Saturation	%	0	500	Analysis Only - 2022-04-04
Specific Conductivity	mS/cm	0	100	6600 Series
Specific Conductivity	mS/cm	0	200	YSI EXOs
Turbidity	NTU	0	4000	YSI EXOs
Turbidity	NTU	0	1000	6600 Series
Turbidity	NTU	0	4000	Analysis Only - 2022-04-04

Discrete Water Quality threshold values
Parameter Name	Units	Low Threshold	High Threshold
Dissolved Oxygen	mg/L	0.000001	22
Salinity	ppt	0	70
Water Temperature	Degrees C	3	40
pH		2	13
Dissolved Oxygen Saturation	%	0.000001	310
Specific Conductivity	mS/cm	0.005000001	100
Turbidity	NTU	0	-
Total Suspended Solids (TSS)	mg/L	0	-
Chlorophyll a uncorrected for pheophytin	ug/L	0	-
Chlorophyll a corrected for pheophytin	ug/L	0	-
Secchi Depth	m	0.000001	50
Light Extinction Coefficient	m^1	0	-
Colored dissolved organic matter, CDOM	PCU	0	-
Fluorescent dissolved organic matter, FDOM	QSE	0	-
Total Nitrogen	mg/L	0	-
Total Kjeldahl Nitrogen TKN	mg/L	0	-
NO2+3 Filtered	mg/L	0	-
NH4 Filtered	mg/L	0	-
Total Phosphorus	mg/L	0	-
PO4 Filtered	mg/L	0	-
Ammonia- Un-ionized (NH3)	mg/L	0	-
Nitrate (N)	mg/L	0	-
Nitrite (N)	mg/L	0	-
Nitrogen, organic	mg/L	0	-

Quality Assurance Flags inserted based on threshold checks listed in Table 1 & 2
SEACAR QAQC Description	Include	SEACAR QAQCFlagCode
Exceeds Maximum threshold. Not verified in raw data	No	2Q
Exceeds Maximum threshold. Verified in raw data	No	3Q
Below Minimum threshold. Not verified in raw data	No	4Q
Below Minimum threshold. Verified in raw data	No	5Q
Within threshold tolerance	Yes	6Q
No defined thresholds for this parameter	Yes	7Q

Value Qualifiers

Value qualifier codes included within the data are used to exclude certain results from the analysis. The data are retained in the data export files, but the analysis uses the Include column to filter the results.

STORET and WIN value qualifier codes

Value qualifier codes from STORET and WIN data are examined with the database and used to populate the Include column in data exports.

Value Qualifier codes excluded from analysis
Qualifier Source	Value Qualifier	Include	Description
STORET-WIN	H	No	Value based on field kit determination; results may not be accurate
STORET-WIN	J	No	Estimated value
STORET-WIN	V	No	Analyte was detected at or above method detection limit
STORET-WIN	Y	No

Discrete Water Quality Value Qualifiers

The following value qualifiers are highlighted in the Discrete Water Quality section of this report. An exception is made for Program 476 - Charlotte Harbor Estuaries Volunteer Water Quality Monitoring Network and data flagged with Value Qualifier H are included for this program only.

H - Value based on field kit determiniation; results may not be accurate. This code shall be used if a field screening test (e.g., field gas chromatograph data, immunoassay, or vendor-supplied field kit) was used to generate the value and the field kit or method has not been recognized by the Department as equivalent to laboratory methods.

I - The reported value is greater than or equal to the laboratory method detection limit but less than the laboratory practical quantitation limit.

Q - Sample held beyond the accepted holding time. This code shall be used if the value is derived from a sample that was prepared or analyzed after the approved holding time restrictions for sample preparation or analysis.

S - Secchi disk visible to bottom of waterbody. The value reported is the depth of the waterbody at the location of the Secchi disk measurement.

U - Indicates that the compound was analyzed for but not detected. This symbol shall be used to indicate that the specified component was not detected. The value associated with the qualifier shall be the laboratory method detection limit. Unless requested by the client, less than the method detection limit values shall not be reported

Systemwide Monitoring Program (SWMP) value qualifier codes

Value qualifier codes from the SWMP continuous program are examined with the database and used to populate the Include column in data exports. SWMP Qualifier Codes are indicated by QualifierSource=SWMP.

SWMP Value Qualifier codes
Qualifier Source	Value Qualifier	Include	Description
SWMP	-1	Yes	Optional parameter not collected
SWMP	-2	No	Missing data
SWMP	-3	No	Data rejected due to QA/QC
SWMP	-4	No	Outside low sensor range
SWMP	-5	No	Outside high sensor range
SWMP	0	Yes	Passed initial QA/QC checks
SWMP	1	No	Suspect data
SWMP	2	Yes	Reserved for future use
SWMP	3	Yes
SWMP	4	Yes	Historical: Pre-auto QA/QC
SWMP	5	Yes	Corrected data

Water Column

The water column habitat extends from the surface of all water bodies to the bottom sediments and encompasses the different features found in the water at different depths (National Oceanographic Center, 2016). The water column habitat must be viewed in relation to its interconnectedness with other habitats. A healthy water column is an integral component in ensuring a healthy marine and coastal ecosystem. Having a flourishing marine and coastal ecosystem in Florida is necessary to support a strong economy. The health of the water column is dependent upon factors as diverse as land use (e.g., agriculture, mining, forestry practices); human population growth; emissions, (e.g., power plants, automobiles, wastewater); climate (e.g., rainfall, temperature, winds and currents); and decadal trends (e.g., El Niño/La Niña, Atlantic Multidecadal Oscillation, climate change).

The water column is composed of various physical, chemical and biological features, and only a small number of them are adequately monitored. Features of the water column that are monitored are used as indicators of the water column health and help assess the status of other habitats. These indicators include nutrient concentrations (nitrogen and phosphorus); water quality (dissolved oxygen, temperature, salinity and pH); water clarity (Secchi depth, turbidity, chlorophyll-a and colored dissolved organic matter); and nekton (fish, macroinvertebrates and megafauna).

Seasonal Kendall-Tau Analysis

Indicators must have a minimum of five to ten years, depending on the habitat, of data within the geographic range of the analysis to be included in the analysis. Ten years of data are required for discrete parameters, and five years of data are required for continuous parameters. If there are insufficient years of data, the number of years of data available will be noted and labeled as “insufficient data to conduct analysis”. Further, for the preferred Seasonal Kendall-Tau test, there must be data from at least two months in common across at least two consecutive years within the RCP managed area being analyzed. Values that pass both of these tests will be included in the analysis and be labeled as Use_In_Analysis = TRUE. Any that fail either test will be excluded from the analyses and labeled as Use_In_Analysis = FALSE.

Water Quality - Discrete

The following files were used in the discrete analysis:

Combined_WQ_WC_NUT_Chlorophyll_a_corrected_for_pheophytin-2024-Mar-27.txt
Combined_WQ_WC_NUT_Chlorophyll_a_uncorrected_for_pheophytin-2024-Mar-27.txt
Combined_WQ_WC_NUT_Colored_dissolved_organic_matter_CDOM-2024-Mar-27.txt
Combined_WQ_WC_NUT_Dissolved_Oxygen-2024-Mar-27.txt
Combined_WQ_WC_NUT_Dissolved_Oxygen_Saturation-2024-Mar-27.txt
Combined_WQ_WC_NUT_pH-2024-Mar-27.txt
Combined_WQ_WC_NUT_Salinity-2024-Mar-27.txt
Combined_WQ_WC_NUT_Secchi_Depth-2024-Mar-27.txt
Combined_WQ_WC_NUT_Total_Nitrogen-2024-Mar-27.txt
Combined_WQ_WC_NUT_Total_Phosphorus-2024-Mar-27.txt
Combined_WQ_WC_NUT_Total_Suspended_Solids_TSS-2024-Mar-27.txt
Combined_WQ_WC_NUT_Turbidity-2024-Mar-27.txt
Combined_WQ_WC_NUT_Water_Temperature-2024-Mar-27.txt

Dissolved Oxygen - Discrete Water Quality

Dissolved Oxygen (DO) is a key indicator of water quality. Oxygen enters surface waters by air-sea gas exchange, by wind action, or as a byproduct of aquatic plant photosynthesis. The actual quantity of DO in aquatic environments is dependent on the above processes as well as water temperature and salinity.

Seasonal Kendall-Tau Trend Analysis
Discrete Water Quality
Map showing location of Discrete sampling sites for Dissolved Oxygen

The bubble size on the above plots reflects the amount of data available at each sampling site

Programs contributing data for Dissolved Oxygen
ProgramID	N_Data	YearMin	YearMax
5002	698	1996	2023
5058	266	2009	2011
3001	98	1999	2003
95	71	1972	2018
103	14	1970	1970
69	2	1998	1998

Program names:

5002 - Florida STORET / WIN
5058 - Southeast Florida Coral Reef Initiative (SEFCRI) Water Quality Monitoring Report
3001 - Lagoon Watch (Formerly Marine Discovery Center)
95 - Harmful Algal Bloom Marine Observation Network
103 - EPA STOrage and RETrieval Data Warehouse (STORET)
69 - Fisheries-Independent Monitoring (FIM) Program

There are no qualifying Value Qualifiers for Dissolved Oxygen in Southeast Florida Coral Reef Ecosystem Conservation Area

Dissolved Oxygen Saturation - Discrete Water Quality

Seasonal Kendall-Tau Trend Analysis
Discrete Water Quality
Map showing location of Discrete sampling sites for Dissolved Oxygen Saturation

The bubble size on the above plots reflects the amount of data available at each sampling site

Programs contributing data for Dissolved Oxygen Saturation
ProgramID	N_Data	YearMin	YearMax
5002	171	1996	2023
3001	98	1999	2003
102	2	1995	1995
95	1	2016	2016

Program names:

5002 - Florida STORET / WIN
3001 - Lagoon Watch (Formerly Marine Discovery Center)
102 - National Status and Trends Mussel Watch
95 - Harmful Algal Bloom Marine Observation Network

There are no qualifying Value Qualifiers for Dissolved Oxygen Saturation in Southeast Florida Coral Reef Ecosystem Conservation Area

Salinity - Discrete Water Quality

Salinity is a measure of the amount of salt in the water. In estuarine ecosystems, salinity is influenced by precipitation, evaporation, surface-water inputs, and exchange with coastal waters.

Seasonal Kendall-Tau Trend Analysis
Discrete Water Quality
Map showing location of Discrete sampling sites for Salinity

The bubble size on the above plots reflects the amount of data available at each sampling site

Programs contributing data for Salinity
ProgramID	N_Data	YearMin	YearMax
5002	816	1996	2023
5058	266	2009	2011
95	230	1972	2018
3001	102	1999	2003
3	76	1998	2022
118	23	2015	2020
69	8	1997	1998
102	2	1995	1995

Program names:

5002 - Florida STORET / WIN
5058 - Southeast Florida Coral Reef Initiative (SEFCRI) Water Quality Monitoring Report
95 - Harmful Algal Bloom Marine Observation Network
3001 - Lagoon Watch (Formerly Marine Discovery Center)
3 - Atlantic Oceanographic and Meteorological Laboratory (AOML) South Florida Program Synoptic Shipboard Surveys
118 - National Aquatic Resource Surveys, National Coastal Condition Assessment
69 - Fisheries-Independent Monitoring (FIM) Program
102 - National Status and Trends Mussel Watch

There are no qualifying Value Qualifiers for Salinity in Southeast Florida Coral Reef Ecosystem Conservation Area

Secchi Depth - Discrete Water Quality

Secchi depth is a measure of the transparency or clarity of the water by a device called a Secchi disk. A Secchi disk is a black and white disk that is lowered into the water on a cord. The Secchi depth is the depth at which the disk can no longer be seen. The deeper the Secchi depth, the greater the water clarity.

Seasonal Kendall-Tau Trend Analysis
Discrete Water Quality
Map showing location of Discrete sampling sites for Secchi Depth

The bubble size on the above plots reflects the amount of data available at each sampling site

Programs contributing data for Secchi Depth
ProgramID	N_Data	YearMin	YearMax
5033	4797	2016	2021
103	961	2020	2021
3001	99	1999	2003
69	8	1997	1998
5002	1	2023	2023

Program names:

5033 - Southeast Florida Water Quality Assessment Survey
103 - EPA STOrage and RETrieval Data Warehouse (STORET)
3001 - Lagoon Watch (Formerly Marine Discovery Center)
69 - Fisheries-Independent Monitoring (FIM) Program
5002 - Florida STORET / WIN

Value Qualifiers

N_Total is total amount of data for a given year
N_ is the total amount of values flagged with the respective value qualifier in a given year
perc_ is the percent of data flagged with the respective value qualifier as a proportion of N_Total

Value Qualifiers for Secchi Depth
Year	N_Total	N_S	perc_S
2023	1	1	100

Note: ¹S - Secchi disk visible to bottom of waterbody

Programs containing Value Qualified data:

5002 - Florida STORET / WIN

Total Phosphorus - Discrete Water Quality

Seasonal Kendall-Tau Trend Analysis
Discrete Water Quality
Map showing location of Discrete sampling sites for Total Phosphorus

The bubble size on the above plots reflects the amount of data available at each sampling site

Programs contributing data for Total Phosphorus
ProgramID	N_Data	YearMin	YearMax
5033	8353	2017	2021
103	1846	2020	2021
5002	664	2013	2023
5058	268	2009	2011

Program names:

5033 - Southeast Florida Water Quality Assessment Survey
103 - EPA STOrage and RETrieval Data Warehouse (STORET)
5002 - Florida STORET / WIN
5058 - Southeast Florida Coral Reef Initiative (SEFCRI) Water Quality Monitoring Report

Value Qualifiers

N_Total is total amount of data for a given year
N_ is the total amount of values flagged with the respective value qualifier in a given year
perc_ is the percent of data flagged with the respective value qualifier as a proportion of N_Total

Value Qualifiers for Total Phosphorus
Year	N_Total	N_I	perc_I	N_Q	perc_Q	N_U	perc_U
2013	62	57	91.9
2014	361	28	7.8			1	0.3
2017	631	48	7.6	556	88.1	2	0.3
2018	1896	149	7.9	386	20.4	113	6.0
2019	2397	170	7.1	3	0.1	26	1.1
2020	2475	165	6.7	6	0.2	23	0.9
2021	2800	47	1.7			5	0.2

Note: ¹I - Reported value is greater than or equal to lab method detection limit, but less than quantitation limit ²Q - Sample held beyond the accepted holding time ³U - Compound was analyzed for but not detected

Programs containing Value Qualified data:

5033 - Southeast Florida Water Quality Assessment Survey
5002 - Florida STORET / WIN

Water Temperature - Discrete Water Quality

Temperature determines the capacity of water to hold oxygen. Cooler water can hold more dissolved oxygen because water molecules are more tightly packed, making it harder for oxygen to escape. Additionally, as water temperature increases, fish and other aquatic organisms become more active and consume oxygen at a faster rate.

Seasonal Kendall-Tau Trend Analysis
Discrete Water Quality
Map showing location of Discrete sampling sites for Water Temperature

The bubble size on the above plots reflects the amount of data available at each sampling site

Programs contributing data for Water Temperature
ProgramID	N_Data	YearMin	YearMax
5002	820	1996	2023
5058	266	2009	2011
95	258	1972	2018
3001	104	1999	2003
103	17	1970	1970
69	8	1997	1998
102	2	1995	1995

Program names:

5002 - Florida STORET / WIN
5058 - Southeast Florida Coral Reef Initiative (SEFCRI) Water Quality Monitoring Report
95 - Harmful Algal Bloom Marine Observation Network
3001 - Lagoon Watch (Formerly Marine Discovery Center)
103 - EPA STOrage and RETrieval Data Warehouse (STORET)
69 - Fisheries-Independent Monitoring (FIM) Program
102 - National Status and Trends Mussel Watch

There are no qualifying Value Qualifiers for Water Temperature in Southeast Florida Coral Reef Ecosystem Conservation Area

Water Quality - Continuous

The following files were used in the continuous analysis:

Combined_WQ_WC_NUT_cont_Dissolved_Oxygen_SE-2024-Mar-23.txt
Combined_WQ_WC_NUT_cont_Dissolved_Oxygen_Saturation_SE-2024-Mar-23.txt
Combined_WQ_WC_NUT_cont_pH_SE-2024-Mar-23.txt
Combined_WQ_WC_NUT_cont_Salinity_SE-2024-Mar-23.txt
Combined_WQ_WC_NUT_cont_Turbidity_SE-2024-Mar-23.txt
Combined_WQ_WC_NUT_cont_Water_Temperature_SE-2024-Mar-23.txt

Map showing Continuous Water Quality Monitoring sampling locations within the boundaries of Southeast Florida Coral Reef Ecosystem Conservation Area. Sites marked as Use In Analysis are featured in this report.